The War
by DramaLexy
Summary: They may have won the battle, but the war has just begun. Post 'The Real World'. Weir centric with some Sparkyness.
1. Chapter 1

TITLE: The War

AUTHOR: DramaLexy

SUMMARY: They may have won the battle, but the war has barely begun. Post "The Real World" Weir-centric with some Sparky-ness

DISCLAIMER: If they were mine… grins evilly

AUTHOR'S NOTE: I thought the end of the episode was just a little too neatly wrapped up. So I decided to continue the story. Enjoy!

* * *

Elizabeth's eyes were downcast as Carson finished giving her a final check-up before releasing her from the infirmary. He offered her a little smile. "You ready to get out of here, luv?" he gently asked. 

She mirrored a much smaller version of his smile. "How could you tell?"

"My first advice would be to get some food in you. I'll come and check on you later this afternoon – I better not find you working in your office." She nodded. "All right, off you go, then."

Elizabeth looked across the room to where Sheppard was lying in a second quarantine area. "Is he going to be okay?" she asked Carson as she stood up.

"I believe so. I don't think the nanites – organic or not – have been able to override their initial programming to keep them from harming Ancients. The ATA gene protected him."

John caught her looking at him and gave her a little wave. She smiled in return. "I'm glad," she quietly told Beckett before leaving the infirmary.

* * *

Upon reaching the mess hall, Elizabeth realized she actually was starving. Even if her ordeal had only been a matter of hours, not days and weeks, that still meant she hadn't eaten all morning and afternoon. Once she'd gotten a tray, she saw Teyla and Ronon sitting at a table by the window. The Athosian waved her over to join them. 

"How are you feeling?" she asked as Elizabeth sat down.

"All right, I guess…It's a little strange to be here after spending so much time getting convinced that Atlantis didn't exist."

"We're glad to have you back," Ronon told her. Elizabeth smiled.

"Thank you." A thought dawned on her. "If all of you have been in the infirmary all day, who's been running the city?"

Teyla smiled. "I was not downstairs all morning. Rest assured; Atlantis is not on the verge of sinking back into the ocean."

Elizabeth laughed slightly. "That's good to know."

"Dr. Weir," a voice called. As Elizabeth turned around, her eyes widened in shock as she found herself not in the mess hall, but in the common room of the mental hospital outside D.C. She closed her eyes, blocking out the image. "Dr. Weir?"

As she looked up, she saw Lieutenant Cadman approaching her table. She was back in Atlantis again, like nothing had ever happened. Everyone was looking at her a bit concernedly. "Y-yes?"

Cadman smiled. "I just wanted to say it's good to see you're doing better." She held up a file folder. "Should I give this to you or – "

"I will take it," Teyla told her. "Dr. Weir is not yet back on duty." Cadman nodded, handing her the report.

"Okay. I'll see you guys later, then." She headed off to get some food for herself.

"Are you all right?" Teyla asked Weir, noticing the look on her face.

"Y-yeah. I'm fine."

* * *

"It's good to have you back in the real world," Sheppard told Elizabeth as they stood together in the control room. She smiled. 

"Thank you."

"Unless, of course, I've been infected by nanites, in which case – "

"John," she cut him off. "Don't." She knew this wasn't his artificial reality, but she still wasn't so sure that it was real for her. He'd been her beacon to guide her out of the confusion in her mind, and at that moment, she didn't think she had the strength to do the same for someone else.

"Sorry," he said a bit sheepishly, realizing his joke had been way off the mark. Not knowing if staying would make things better or if he'd open his mouth again and make them worse, he decided to move away, heading back downstairs.

Elizabeth was left standing alone on the balcony, staring down at the quiet Stargate and fingering her father's pocket watch. To tell the truth, she was tired, but was so desperately afraid of going to sleep. Would she still be on Atlantis when she awakened?

"I'll see you in the morning," she finally turned and told the officers on duty in the control room. They nodded to her in acknowledgement. However, she wasn't quite ready to go back to her room yet.

* * *

Out on the balcony, the sea breeze played with her hair, making it dance around her head. She hadn't worn it longer than shoulder length in years, but she liked it. The wind was also taking away the tears that slowly rolled down her face. Hardly anyone had ever seen her cry before, mainly just her mother. Helen Weir had been there to hold her the first time she'd had her heart broken by a boy, when the stress of her triple major in college had finally gotten to her, when her father had died, when she'd been in the hospital – 

Elizabeth froze as she realized that the last event on that list hadn't happened. She hadn't seen her mother since she'd been home the previous year; her last trip to Earth had been too brief to even leave Cheyenne Mountain. Rationally, she knew it would take time to get past the day – weeks! – that she'd just experienced, but some part of her wished it would all just be erased. She didn't want to remember; how dare the replicators have done that to her?

She closed her eyes tightly as a sudden migraine came on, stumbling backwards away from the railing. The pain intensified, and the last thought Elizabeth had before succumbing to the darkness that overwhelmed her was that she hoped she would wake up.

Throughout her body, the nanites began replicating…

* * *

TBC... 


	2. Chapter 2

John stopped by the control room again before turning in for the night, and was glad to see on first glance that Elizabeth wasn't there. "Did Dr. Weir turn in for the night?" he asked one of the Lieutenants in the room.

"She said she'd see us in the morning, Colonel," he replied. John nodded.

"All right then. 'Night, gentlemen."

"Goodnight, sir."

John was on his way back to the staircase when some sixth sense made him take a look out the door to the balcony. Nothing seemed amiss at first, but then he noticed a shadow on the dimly lit deck that shouldn't have been there. A shadow in a red tee-shirt. Sheppard waved his hand at the door panel to open it.

"Elizabeth?" he called as he realized it was her sprawled form on the ground. She didn't move. John tapped his earpiece. "Sheppard to Beckett."

"Go ahead, Colonel."

"I need a med team on the balcony outside the control room, now."

"What happened?"

"It's Elizabeth, I think she passed out or something…At least I'm hoping she only passed out." Kneeling beside her, he cradled her head in his lap.

"We'll be right there," Carson told him.

"Elizabeth, can you hear me?" John asked her, taking her hand. "Come on; don't do this to me again. Open your eyes." After an eternal moment, her eyelids started to flutter. "Hey, that's it."

"John?"

"Yeah. You scared me for a minute there." He helped her sit up.

"Where are we?"

"On the balcony. Take it easy; Carson's gonna be here in a sec."

Elizabeth looked around, concerned, studying everything around them. John could barely make out the question she asked him in the smallest, most vulnerable-sounding voice he'd ever heard: "This is real, right?" He held her hand a little tighter.

"Yeah. It's real. I'm right here; you're going to be okay. You probably have just been pushing yourself a little too hard. It's been quite a day." She just nodded at that.

"Yes, it has."

* * *

"I'd say you have a clean bill of health, my dear," Carson told Elizabeth as the Lantean scanner stopped and she got up from the bed. "It appears that the nanites are still dormant." 

"You're sure?" John asked. Carson pointed to the screen for proof. The little dots visible in her scan weren't emitting energy signals that would indicate activity.

"We're still working on a way to neutralize them completely. In the meantime, I suggest you remember that your body's been through quite a trauma and go easy on it. Getting some sleep probably wouldn't be a bad idea." Elizabeth slowly nodded.

"Thank you, Carson."

"No problem, luv. Come see me in the morning and we'll do another scan, just to be safe."

John chivalrously offered his arm. "Come on, I'll walk you to your room."

* * *

They talked about anything BUT what had happened that day on the walk. Rodney's latest experiment, the little football games that John was organizing, the changing seasons on the planet. When they finally reached Elizabeth's door, she smiled a bit awkwardly as she waved at the console to get in. "Thanks for walking me back," she said. "And finding me in the first place." 

"It might have been a bit of a chilly night otherwise," he responded with a smile.

"Yes, well…luckily it won't be. Sleep well."

"You, too." John started walking down the hall, so Elizabeth went inside. She didn't see him stop at the corner and wait, unable to leave without really making sure that she was okay.

Elizabeth got changed out of the clothes she'd put on that afternoon and curled up on her bed. A small console on the nightstand controlled the lights, and she reached to turn them off. Being surrounded by the black night, however, wasn't comforting. Every time she closed her eyes and opened them again, she wasn't sure if she was simply still awake in her room, or if she'd gotten pulled into the pit of nothingness that lurked in her mind. Fear flooded through her – she didn't want to get pulled back down. She wanted to stay!

John had seen her room go dark, and turned away to walk to his own quarters. He noticed out of the corner of his eye when the light came back on. Stepping back over to the door, he tried to peer through the stained glass to see if Elizabeth had gotten up, if something was wrong, but as far as he could tell she was still in bed.

He waited a few minutes, just to make sure, and sighed to himself as he walked away. As if she needed another struggle in her life to deal with.

* * *

TBC... 

Thanks for the reviews I've gotten so far! Feedback is always appreciated.


	3. Chapter 3

By the next morning, there was nothing Elizabeth wanted more than to get back to life in the city as usual. She needed something to keep her mind occupied instead of dwelling on the nightmare that she'd been living the day before. "Morning, Dr. Weir," the staff in the control room told her as she came up the stairs.

"Good morning. How are things going around here today?"

"AG-4 and AG-7 are both going off-world," Campbell, one of the technicians, told her. "Other than prep-work for that, things are pretty quiet." Elizabeth nodded.

"Sounds good. I'll be in my office if anyone comes looking for me."

"Yes, ma'am."

* * *

As she sat down at her desk, Elizabeth realized the reports she'd been working on the previous morning were still laid out, just as she'd left them. Two more small stacks had been added, along with a note from Teyla marking one pile as reports she'd gone through and believed they only needed final signatures, and the other pile contained files she thought Elizabeth would want to look at herself. She made a mental note to thank the Athosian later; Teyla had been doing a great job as of late in stepping into Elizabeth's shoes whenever needed. 

While going through the reports, Elizabeth rubbed her temples as a headache started to come on. She hadn't slept much the previous night, and knew that skipping breakfast on top of that probably hadn't been a great idea, but she was used to going through most of the day without eating. Where were the headaches coming from?

"Elizabeth, what are you doing up here?" a voice asked. She jumped when she looked up and saw Dr. Fletcher standing in her doorway.

Carson frowned, concerned, as he noticed the look of surprise and fear cross her face. "What's the matter? I'm sorry if I startled you – "

Elizabeth shook her head, her vision clearing and allowing her to see who had really come to find her. "It's all right," she told Beckett. "What can I do for you?"

"You can go back to your quarters! You're supposed to be resting, lass."

"I couldn't stay there anymore. I just needed to do something to keep busy, and there's always plenty to do around this city." Beckett sighed.

"I'd like you to talk with Kate."

"Carson, I'm fine."

"She'll be expecting you this afternoon at 1400 hours."

A stab of pain went through Elizabeth's head and she no longer felt up to the challenge of arguing. "Fine," she muttered, rubbing at her forehead.

"Are you all right?" Carson asked.

"It's just a headache…I probably need to eat something."

"I can ask someone to bring you a tray from the mess."

"Thank you."

"It's no problem. Let me know if you have any other symptoms, all right?"

* * *

One of the military men brought up some lunch to Elizabeth's office, although she mainly wound up only picking at it. She considered skipping out on her appointment with Dr. Heightmeyer, but really didn't want to have to deal with Carson later on. 

"How are you feeling?" the blonde psychiatrist asked as they sat down in her office.

"All right…A little tired."

"Would I be wrong if I guessed that you didn't sleep very well last night?" Kate asked with a little smile.

"No," Elizabeth finally admitted.

"That's okay, Elizabeth. It's to be expected. Were you having dreams?"

"I don't remember," she lied. Kate slowly nodded.

"Can we talk about the things that happened to you while you were unconscious yesterday?"

"Like what?"

"You told Carson that you were back on Earth, and the nanites were trying to convince you that Atlantis and the Stargate had never existed?" She nodded. "Did you believe it?"

Elizabeth thought about that. "I'm not sure…I think I wanted to. If I couldn't get back to Atlantis then I wanted to get back to life as normal on Earth."

"What was that life like?"

"Teaching political science. Living in DC with my dog. It was the life I had before I learned about the Stargate and Ancients and aliens."

"Do you miss it?"

"Sometimes…but after living in it again, I think that I miss Atlantis more."

A lightning bolt of pain shot through her head. Kate watched, concerned, as Elizabeth pressed the palm of her hand to her forehead, closing her eyes. "Elizabeth? Are you all right?"

Her hand fell away and her eyes opened, but she didn't look up. Kate started to get worried as she saw that her eyes were glazed over, empty. "Elizabeth?" Nothing. Kate tapped her headset. "Dr. Heightmeyer to Dr. Beckett."

"Go ahead, Kate."

"We've got a problem."

* * *

TBC... 


	4. Chapter 4

The last thing that John wanted to see when he walked into the infirmary was Elizabeth Weir back in an isolation room. She was still as a statue on the bed as the scanner moved back and forth above her. John never wanted to see that sight again.

"What the hell happened?" he tightly asked Carson as the doctor approached him.

"The nanites have become active again. I'm actually wondering if they've actually been going in and out of a dormant state for the past day, replicating in small bursts. Now, they are fully active and multiplying, although mainly staying within her brain."

"Is she unconscious again?"

"Possibly worse. She's near catatonic, but I believe some part of her is still aware of what's going on around her. She just can't break free to the surface."

"We've really gotta get rid of these damn things," John growled.

Carson nodded. "I know. We're still working on a solution."

"Do you know what's happening to her? Is she dreaming again, do they have her trapped somewhere?"

"I can't be certain. Her mind isn't showing the same activity levels as last time, but I have no idea what that means in terms of what the nanites are making her see or feel."

John sighed in frustration. "I have to go in there. I have to try bringing her back again. It worked before – "

"I know, Colonel. You weren't going to get an argument from me…Keeping her with us may be the only thing that can keep her hanging on long enough to fix this."

* * *

John needed a little bit of a walk (and a couple wacks on a punching bag in the gym) before he went in to see Elizabeth. He'd made the mistake of being too upset when he'd initially talked to her the last time, and had overheard her telling Beckett that he'd first scared her before he'd been able to help her out of the dream world. John couldn't afford to do that again. 

Upon re-entering the infirmary, he stepped into the isolation area, pulling the curtain closed behind him. He just stopped for a moment and watched the woman sitting up on the bed before him. She didn't move, didn't look at him. He could barely tell she was breathing. "Elizabeth?" he quietly asked, without getting a response. He stepped forward, taking her hand in his. "Hey, 'Lizbeth, can you hear me?"

Slowly, ever so slowly, her head turned until her hazel eyes met his green ones. John smiled. "Hi. I thought that you were in there somewhere." She didn't say anything. "You hungry? I got a little bit of stuff from the mess. Just applesauce and some juice; I wasn't sure if you'd eaten today or if you'd done your normal routine of only eating when forced to." No response. "Okay, maybe not hungry…"

He suddenly realized that her fingers were like ice within his own. "Are you cold? Here – " he picked up a blanket off the bed and wrapped it around her shoulders, gently rubbing her arms to try and transfer some warmth. "That's better, huh?" They sat together for a few moments, not a word being spoken. "You know, this silent treatment's gonna wear thin," he tried to joke. "Why don't you just tell me what I'm in the dog house for this time? Come on, go ahead and yell. I won't say a word back, I promise. How often are you gonna get a deal like that?"

Elizabeth looked away from him, going back to staring at nothing. He sighed, sinking down into the chair beside her bed.

* * *

They stayed together in silence for what seemed like eternity. Sheppard was almost starting to nod off when he heard her voice. "John?" 

A smile crossed his face. "Hey, welcome back."

"What…what happened?"

"You got a little lost, I think. Do you remember anything?"

She shuddered slightly as she thought about it. "It was just…dark. How long was I like that?"

He checked his watch. "A couple hours." He got up from the chair, heading for the opening in the curtain around them. "I should go and tell Carson you're okay."

"I'm not," she said, stopping him in his tracks.

"What?"

"I'm not okay…they keep trying to pull me under, John, and I'm terrified that they're going to succeed."

In that moment, he suddenly realized just what the replicators were trying to do. They hadn't been able to break her while unconscious, so they'd found a new weapon. The terror they could inflict in the real world was threatening to succeed where their fake reality had failed.

John stepped forward, giving her hand a squeeze. "They won't. I promise."

* * *

TBC... 


	5. Chapter 5

Beckett wasn't about to let Elizabeth out of the infirmary with the nanites active in her body. Anyone with the ATA gene was protected, but he really didn't need to have to deal with an epidemic of infections by the organic micro-machines, considering the fact that they still didn't have a treatment.

John stayed with Elizabeth for the rest of the day, unable to bring himself to leave her alone. He semi-jokingly told her that he would be her anchor, but he actually was afraid that she would slip away if he wasn't looking and get pulled off to somewhere he couldn't bring her back from.

"You don't have to stay here all night," Elizabeth told him as it started to get pretty late. John shrugged.

"The alternative would be the stack of paperwork on my desk, so…" They both smiled. "You think you're going to be able to go to sleep?"

"I don't know."

"Carson was saying earlier he could give you something to make sure you don't dream."

"You mean naturally," she pointed out. "I don't think there's anything he could do about dreams caused by the machines in my head."

"True…but it might be better than nothing."

Elizabeth shook her head. "I don't want a sedative."

John picked up the pudding cup that had been part of the dinner that had been brought for Elizabeth a few hours earlier. "You going to eat this?" he asked. She shook her head. He'd already polished off his own meal, while she'd barely touched hers. Carson was going to start threatening her with feeding tubes pretty soon, but she couldn't force herself to have an appetite.

"Aren't you supposed to be going off-world tomorrow?" she asked, lying on her side on the bed.

John shrugged, putting a spoonful of his pudding in his mouth. "Lorne can handle it. He's been wanting more missions anyway."

"What about the rest of your team?"

"Rodney's working with Carson. Teyla's covering for you and Ronon's bullying anyone who doesn't want listen to her. I think they're all occupied. So sending AG-2 instead works best for everyone."

Elizabeth sighed. "I want this to be over. I want everything to just go back to normal…Whatever normal is for this city."

John smiled. "It will. You've just got to keep fighting, okay? The galaxy-renowned Dr. Weir doesn't give up." That got her to crack a smile.

"Two galaxies."

"Oh, yes, sorry. My mistake. Bi-galaxy-renowned." He returned the empty pudding cup and spoon to the mess hall tray. "The Doc's going to read me the riot act if you don't at least try to go to sleep."

"All right, all right," she gave in. John got up, slipping out of the isolation room to dim the lights. "John? Could…could you leave them on?"

He mentally kicked himself. "Yeah, sure…Sleep well; I'll see you in the morning, okay?"

"Yeah. Goodnight." Elizabeth watched him leave, trying to gather the courage to attempt going to sleep. After a few minutes of quiet, however, her body didn't give her a choice in the matter and the exhaustion the past few days had brought overtook her.

* * *

Elizabeth woke up the next morning to the sound of the machines that surrounded her, constantly checking on her condition. As promised, John was sitting beside her bed, and he smiled when he saw she was awake. "Hey, good morning. You okay? No nightmares?" She shook her head. "See, you really are stronger than them. The Doc should be over in a minute to check on you. You want some breakfast?" He indicated a tray that he'd brought. 

"Maybe a little." He handed her the plate of eggs, bacon, and a biscuit.

"We actually got the good stuff from home today," he joked.

Elizabeth smiled. "That's rare," she replied in kind. "Who'd you have to bribe?" John laughed.

The sound of the zipper on the curtain alerted them to the fact that someone else was entering the isolation room. "How are you feeling this morning?" a voice asked, and Elizabeth was shocked to look up and see Dr. Fletcher instead of Beckett.

"What's the matter?" John asked her. She closed her eyes, but he didn't go away. Fletcher moved toward her, but she jumped away, knocking her plate from her lap.

"Stay away from me!"

"Elizabeth, what's wrong?" John asked. "The Doc's going to help you."

She shook her head. "This isn't real. I'm still asleep; this isn't real!"

Fletcher smiled. "It's real enough."

* * *

Sheppard smiled at the nurses as he came into the infirmary. "Is Dr. Weir still asleep?" he asked one of them. She nodded. 

"Last I saw."

John let himself into the isolation room, putting down the tray of food that he'd brought for breakfast. He didn't mind waiting for her to wake up, knowing that sleep probably hadn't come easily the night before. As he sat down in the chair by her bed, however, he noticed that her hands were clenched tight in fists. Blood was actually escaping cuts from her nails on one hand.

"Elizabeth?" he asked, shaking her shoulder. She didn't wake up. He tried to pry her fingers open, but her muscles were completely tense. _Oh, God, I shouldn't have left…_ "Elizabeth, wake up!"

* * *

TBC... 

Yes, another cliffhanger. I seem to like those or something...


	6. Chapter 6

John spent the morning in the infirmary, just watching Elizabeth from outside her isolation area as the scanner moved back and forth and the doctors and nurses made sure she was still breathing and her heart was still pumping. She'd finally relaxed and they'd been able to bandage her hands, but no one could wake her up.

"I think we've got something," Carson told him as he approached. "It may not work, but at least it's something to try."

"Anything's better than this," John muttered.

"Why are you immune to the nanites? Why am I?"

"The ATA gene," he replied. "But you tried the treatment two years ago on Elizabeth; it didn't work."

"I know. The therapy delivers the Ancient gene straight to the cells of a person who wasn't born with it. If the nanites detect this gene, their programming automatically makes them think the person is an Ancient and therefore cannot be harmed."

"I know that part already. Any nanites in that person would automatically become permanently dormant."

"We think we could trick them into believing that Elizabeth has the ATA gene without her cells actually having to accept the treatment – we use blood cells."

John realized where he was going with this. "You give her blood from someone with the gene, and the nanites might not know the difference?"

"Exactly. At this point, we've got to try it."

"Who in the city is a match?" John asked.

"For starters, lad, you are."

* * *

Elizabeth just stared at the two men in front of her. John couldn't be part of the dream; he was supposed to be the person helping her, not pulling her in. The nanites had learned too much – they knew exactly what was going to drive her past the break point. A part of her almost wanted to let them, to end everything they'd put her through, but she couldn't. No one in the real world was going to be able to save her if she didn't fight for herself.

She ripped the IV out of her hand, and pushed past Fletcher and 'John,' getting out of the isolation room and then the infirmary as fast as she could. She could hear them behind her, radioing for guards and chasing her down. She needed to find a teleporter, to get away…

Running into the small closet-like room, she pushed an icon on the screen for the destination farthest from her current location. The doors closed just in time. Finding herself on the outskirts of the east pier, she started looking for somewhere to go, somewhere to hide. Eventually they would find her.

* * *

John looked across the infirmary from his seat by the monitors to look at Elizabeth. Her mind was active; they knew that the nanites were doing something to her, they just had no idea what. He didn't want to imagine it.

"Are you ready to do this yet?" he snapped at Carson, his voice a little more harsh than he'd intended. The doctor let it go.

"Aye," was all he said as he began hooking up the equipment he needed. Sheppard watched as the needle went in his arm. This HAD to work. He had the strongest control over Ancient technology of anyone in the city. If he couldn't help her, no one else would be able to do it better.

Once they'd gotten enough blood, it was taken over to be given to Elizabeth. The bag was hung on a stand and connected to her IV. It HAD to work.

* * *

Elizabeth was holed up in a small room with an ocean view, pacing as she tried to figure out what came next. Walking through the gate wasn't going to help her this time – she was already 'home' where she belonged. They were taking advantage of that. She had nowhere to run to.

She jumped as another figure suddenly appeared in the room, starting to get up to run again. "Elizabeth, it's going to be okay," John told her. "We figured out a way to help you."

She shook her head. "I'm not listening to you; I'm not going to let you trick me."

"It's me, 'Lizbeth. I'd never hurt you." And she wanted so badly to believe it.

* * *

The medical team was taken by surprise when Elizabeth's whole body suddenly went tense, raising slightly off the bed. Her muscles relaxed for a moment, then tensed again. "She's seizing!" Carson realized and the doctors rushed to help.

John got up from his seat, moving over to the curtain to the isolation room. "You've gotta keep fighting," he told her. "Come on, you can do it…"

"It's getting worse," Beckett observed. "We've got to stop." He reached for her IV line.

"Don't!" John told him. "They're testing her – and us. She's strong enough to do this; we just have to give her a chance." Stepping around the other doctors, he entered the isolation room and took her hand. "Come on, 'Lizbeth," he murmured, "This worked the last time…"

* * *

TBC... 


	7. Chapter 7

Elizabeth looked up as the door to the room burst open and another John Sheppard came in. "Elizabeth, come with me," he told her, offering a hand. "You'll be safe; I promise."

"Don't listen to him," the real John said.

"You can make this all end," the other one promised. "Just take my hand."

Almost as if she wasn't controlling it anymore, her arm raised. "'Lizbeth, stop," John told her. "Fight them. You know what they're trying to do. Don't let them win. We're trying to help you; you can beat them, you just have to hold out a little while longer."

She closed her eyes, not having to want to deal with the dual visions anymore. "I just want to go home."

"I can take you home, Elizabeth. I can take you anywhere you want to go." With speed that surprised even Sheppard, her hand suddenly shot out and punched the nanite vision in the face. He crumbled away to bits of metal.

"Nice hit," John said with a small smile.

"Thanks."

"You ready?" he asked, holding his hand out to her. Elizabeth nodded and put her fingers within his.

"Let's go."

* * *

John sighed with relief as Elizabeth's seizures finally stopped. Her eyelids fluttered open, and she looked around for a moment, confused. "Morning," he said with a little grin. 

"Hi."

"The nanites appear to be completely dormant," Carson reported, looking at the monitors across the room. "I think it worked."

Elizabeth looked down, realizing that John was still holding her hand. His eyes followed hers, but he made no move to let go, a casual smile on his face. "Thank you," she told him.

"No problem…just, let's not have to do this again."

* * *

After a day of just-to-be-sure tests, Elizabeth was getting really sick of being poked and prodded. It didn't help that half of her nightmare world had also revolved around doctors and needles and drugs. 

"Carson, I really just need to get out of here," she finally wound up telling the Scotsman. "I can come back in the morning if you want to put me under a microscope some more, but I just…I've had enough for the day."

He was a bit taken aback, but none of his tests so far had revealed anything to be concerned about. "All right…Come see me tomorrow and we can finish up and talk about when you could start working again."

"Thank you."

* * *

She got changed into her normal BDU pants and a red long sleeve shirt and got out of the infirmary as quickly as she possibly could. It was dinnertime, and she actually felt hungry for the first time in a couple days, but didn't want to be surrounded by people in the mess hall. It was a little too much, too soon. 

Just as she'd hoped, she found Teyla in one of the training rooms, stretching out after practicing with a couple students. "When were you released from the infirmary?" the Athosian asked her as they sat down together by the window.

"Just now, although I'm sure Carson wishes I was still there."

"He is simply concerned for your well-being, as we all are."

"I know, I just…I really wish none of this had happened at all and I'm sick of the reminders that it did."

Teyla nodded. "I understand."

"Thank you for everything that you've done around the city these past few days. I apologize for anyone who didn't respond well to your leadership."

She smiled. "That is quite all right…I believe that a few of your crew are now somewhat frightened of Ronon, however."

Elizabeth laughed a little. "I wouldn't be surprised. Hopefully Carson will let me get back to work tomorrow."

"Do not worry; we can continue to assist you as you recover…Have you had your evening meal yet?"

"No. I guess I probably should, though."

"I should be meeting with Ronon and John in the mess hall; you are welcome to join us."

She nodded. "Thanks."

* * *

John wound up being ten minutes late to dinner. "There you are!" he said to Elizabeth as he approached the table. "I've been looking all over for you! I brought a tray to the infirmary and found it empty. Why didn't you tell me Carson let you out of lock-up?" 

"Sorry. I just went for a little walk, and wound up talking with Teyla, and now we're here."

"You feel okay?"

"Yes, John, I'm fine. Honest. That's why I got let out of 'lock-up,' as you put it."

"Now that you're finally here," Ronon pointedly said, "Let's get some food." The girls went together to fill their plates from one section of the line, and John and Ronon wound up at the other end. Sheppard didn't miss the look the ex-Runner was giving him.

"What's that smirk for, Chewie?" he asked.

"Nothing. Just you and Dr. Weir."

John raised an eyebrow. "What about us?"

"Sometimes you're like an old married couple." John almost dropped his tray.

* * *

TBC... 


	8. Chapter 8

John walked Elizabeth back to her quarters again that night after dinner and a couple movies in a rec room with the rest of his team. "I guess it's a good thing Daedalus is bringing more of our special food orders this trip," she said with a smile as they made their way through the corridors. They'd eaten the last of their stock of popcorn that evening.

"Yeah. Otherwise I bet Cadman would stick her little chick-flick movie club on my ass."

Elizabeth laughed. "That would be a sight to see."

"Oh, I'm glad you think so!"

They stopped outside her door. "Thank you for everything, John. Really."

"Don't worry about it. I had my own interests in mind, too."

"That so?"

"Yeah. I'd hate to have to live in this city without you."

Elizabeth smiled. "I feel the same way." An awkward silence ensued.

"I'll see you tomorrow morning. You think Carson will clear you for the briefing?"

"I'll be there whether he clears me or not."

John laughed. "You're picking up my bad habits. Goodnight."

"'Night." Elizabeth disappeared inside her room, and John found himself lingering down the hall, wanting to see for himself if she really was doing better. He could see when she stopped moving around her room, and assumed she'd gotten in bed, but the light never went out. Apparently she was pretty good at pretending.

* * *

Elizabeth made it out of the infirmary as fast as she possibly could the next morning and headed up to the control room to meet with her senior staff. A hand-made 'Welcome Back' banner on the wall of the conference room was a nice surprise. 

"Thank you, all of you," she told Ronon, Rodney, John, and Teyla as they sat down. "I'm still reading over all of your reports to get up to speed, but I'm mostly caught up. How did AG-2's mission go yesterday?"

"Well," John told her. "They're interested in opening up trade relations…"

Once the meeting was over, everyone scattered. Rodney escaped back to his lab with Zelenka to work on whatever their latest crazy experiment was. Ronon and Teyla were off in search of a training room, and John claimed he had a stack of paperwork on his desk. Elizabeth went back to her own office to finish up her reports. They were sending an uplink to SGC that afternoon, and she wanted to make sure everything was ready. She was so engrossed in one of the files that a knock on her doorframe completely startled her.

"Sorry, sorry," John said as he saw her jump. "I didn't mean to scare you."

"I-I thought you were down in your office?" Elizabeth said.

"Yeah, I was halfway there when I realized I'd meant to ask if you wanted to get lunch today."

Elizabeth frowned. "You couldn't have just used your radio?"

"I, uh, thought I'd forgotten my tablet in the conference room," he made up on the fly. "But I guess it's in my quarters." In actuality, John had wanted to check up on her, but there was no reason for her to know that.

"Well, call up at lunchtime and I'll see how far I've gotten with this stuff."

"You've gotta eat, Elizabeth."

She sighed. "I've got Carson on my back already, John. I don't need you, too."

He frowned. "I'm just looking out for you."

"Thank you, but I can take care of myself. I've been doing it for years." John decided it wasn't worth picking a fight with her.

"Okay, fine, I'll call up at lunch," he said before turning to leave. Elizabeth put her face in her hands. She hadn't meant to get cross with him, it just happened. She'd apologize later.

John nodded in greeting to Campbell as he walked through the control room. "Do me a favor," he quietly told the technician. "Keep an eye on Dr. Weir this morning."

"Is she okay?" he asked.

"Yeah, I'm probably overreacting; just…I wanna make sure."

* * *

Elizabeth gave in to lunch, hoping it would be a sort of peace offering, and John came up to the control room to meet her. "Anything?" he asked Campbell as he walked through. 

The younger man turned to look toward Elizabeth's office to make sure she wasn't listening. "She's been a little jumpy," he said. "But, if the stories going through the grapevine are true…"

John rolled his eyes. "Don't ever believe the grapevine."

Elizabeth came out of her office. "Ready to go?" she asked John. She seemed fine, just like any other day, but he knew better.

"Yep." As they headed back downstairs, a light bulb went off in John's head. He had an idea on how to help Elizabeth – now he just needed to figure out how to pull it off.

"What's that smile for?" she asked him as she noticed the look on his face.

"Nothing. What time is the upload supposed to be?"

"1600 hours, so get your reports up by 1530 so everything can get packaged."

He grinned. "No problem."

* * *

"Wait, one last thing," Sheppard told one of the techs in the control room as he came up the stairs that afternoon at 1557 hours. He plugged his own tablet laptop into the computer the younger man was sitting at and transferred a file into the package that was about to be sent to Earth. 

"Last minute report, Sir?" the man asked.

John smirked. "Yeah, something like that."

* * *

There was a lot of preparation that went into every Daedalus mission between Earth and Atlantis, and Colonel Caldwell was looking forward to being up in open space again and away from the endless meetings at SGC. 

"Colonel!" he heard a voice say, and turned to see a lieutenant hurrying down the hall behind him. "This is for you, Sir. Came through on today's uplink from Atlantis." He handed over a sheet of paper.

"Thank you," he told him. The lieutenant nodded and headed off the way he'd come. Caldwell's eyebrows knitted as he read over the memo. "Sheppard's lost his mind," he muttered to himself.

* * *

TBC... 

Any guesses on the secret plan? Thank you to everyone who's sent me feedback so far!


	9. Chapter 9

Just about three weeks later, the Daedalus was dropping out of hyperspace in orbit over Atlantis. "Daedalus, this is Flight," one of the city's officers radioed up to the ship. "You're cleared for landing."

"Understood, we have the beacon," Caldwell replied. "I'm request that Colonel Sheppard and Dr. Weir meet us on the north pier."

Both Elizabeth and John were up in the control room, listening to the transmissions. The city's leader frowned upon hearing that last bit. "Is there a problem, Colonel?" she asked.

"No problem, Doctor, I just have some cargo from Earth that needs to be transferred directly to you." Elizabeth looked to John, who shrugged innocently, doing his best choir boy imitation.

"We're on our way."

* * *

By the time they got down to the north pier, crewmen had started unloading the crates of supplies that had been packed onto the ship. "Colonel," Elizabeth greeted the ship's captain as he came through the hatch. 

"Doctor, Colonel," he replied. "I've gotta say, Sheppard, I thought you'd gone off the deep end when I got your request, but whatever you included in that uplink for General Landry must have been pretty damn persuasive."

Elizabeth looked back and forth between them, confused. "What are you talking about?" she asked.

John smiled. "I thought it might do you some good to have an old friend around." That still didn't help to clear things up.

Caldwell turned around, looking back into his ship for someone. "Lieutenant," he called. One of his officers joined them outside – and was holding a leash for a beautiful white dog.

"Sedge!" Elizabeth exclaimed, kneeling to hug the animal as it bounded over. "How did you arrange this?"

"Don't look at me," Caldwell said.

"I called in a favor or two…" John told her. "I guess once Colonel Caldwell agreed to do transportation, it was just a matter of General Landry giving the okay."

"I'm pretty sure the pentagon doesn't know about this," Caldwell added. Elizabeth smiled.

"Thank you both."

"Good surprise?" John asked.

"Yes, excellent."

* * *

Sedge hadn't been cooped up in a cage for the entire three-week trip, but there was still only so much room onboard the Daedalus. The dog thoroughly enjoyed a trip to one of the city's outdoor areas, running back and forth across what had probably been a beautiful lawn 10,000 years earlier. Elizabeth couldn't keep the smile off her face as she watched, tossing a ball for Sedge to chase after. 

"Having fun?" John asked as he stepped out through the sliding stained glass door to join them.

"Yes. Aren't we, girl?" she asked Sedge as the dog bounded over. John petted her head. "What made you think to do this?"

"Well…we all take care of each other around here, and I just thought it might be nice if you had someone watching out for you when the rest of us can't. I know you don't tell us everything, and that's okay. I figure Sedge would probably be a pretty good listener, though, if you needed one."

Elizabeth smiled. "I'm okay, John…or at least I'm getting there."

He studied her for a moment before at last deciding she really was being truthful. "All right then." John stuck his hand out, asking for the ball she was holding. "How good is Sedge at catch?"

"Pretty good."

* * *

That night, after changing into pajamas, Elizabeth curled up in bed with Sedge, gently stroking the dog's fur. "I have definitely missed you," she told the animal. "You probably are a little homesick for Colorado, but that'll go away. I think you'll like it here. I certainly do. You're probably going to be the center of attention for a little bit; I'm sure there are a lot of other people in this city missing the pets they left behind. Everybody's like one really big family in Atlantis – I guess you being here is proof of that, huh? There's at least one person around here that really cares about me…Hopefully someday I'll get the chance to return the favor."

* * *

John had just finished taking a late night run around the city with Ronon and decided to stop by Elizabeth's quarters to see how she was doing. He smiled to himself as he came down the hall and saw that the light in her bedroom was out for the first time in almost a month. 

"'Night, 'Lizbeth," he whispered before turning back and walking away.

* * *

TBC... 

Only one chapter left!


	10. Epilogue

New Year's Day on Atlantis wasn't the same type of holiday as on Earth. Instead of being close to the winter solstice, New Year's was celebrated on the anniversary of the day that the city had risen from the ocean. Supply runs with the Daedalus meant that there was liquor on hand for the event, and a few crewmen would decorate the gateroom and adjacent balcony for the occasion.

On the last evening of their fifth year in Atlantis, John found Elizabeth still in her office – Sedge lounging on the floor underneath her desk – as the festivities got underway. "What are you still doing up here?" he asked as he came in the door.

"I just had a few more things – "

"'Lizbeth. They call it a 'holiday' for a reason."

Elizabeth put down the pen for her tablet. "When exactly did my name lose two syllables?" she asked him with a smile.

"Not sure. But you never told me to stop."

"Mmm, was that my mistake?" she asked as she got up from the desk.

"Yeah, that's it. All your fault."

"Fine, if you insist on dragging me out of here – "

"I do."

" – then let's go."

* * *

They each mingled with the crowd of expedition personnel that were downstairs. The food was good, the company was better, and it was fun to see how much had changed in Atlantis in the past five years. Many couples had formed – Beckett and Cadman were due to be married the next time they went back to Earth – and a few of them were expecting children. In all honesty, Earth was no safer than Atlantis, and Elizabeth had fought hard for the city's right to develop as a real colony, not a tightly controlled military base. 

"Dr. Weir?" she heard a voice ask and turned to see Zelenka approaching. "We are ready." She nodded.

"Go ahead."

Everyone had decided that their fifth anniversary was a special one. A few members of the science team had spent the past few days cooking up homemade fireworks – which sounded more dangerous than it really was, considering the fact that some of them had built atomic bombs before. The party-goers started moving outside to the balcony to watch as bright explosions of color began lighting up the night sky.

As she stood in one of the doorways, John caught Elizabeth's eye from his place out by the railing. He nodded slightly, almost imperceptibly, and she disappeared back inside.

* * *

Five minutes later, he joined her on a balcony a few levels down from the control room. They could still hear the party going on above them, but had gained the ability to watch the fireworks with a bit of privacy. 

"Happy New Year," John quietly said, wrapping his arms around her waist from behind as they both watched the show.

Elizabeth smiled. "Happy New Year." As an afterthought, she pulled her necklace out from underneath her tee-shirt, bringing the object hanging from the silver chain into view: a small diamond ring.

John smiled as he noticed. "One of these days, that'll be on your finger," he promised.

She shrugged. "I like having you as my secret."

"Can you believe it's been five years?" he asked after a few moments of silence. "Half a decade since you plucked me out of McMurdo and into this whole other world."

"I have no clue how I've put up with you for so long," she teased, earning a poke in the side. "Seriously, though. In the first year of this little 'camping trip,' I'm sure everyone thought we would have killed each other before we would get married."

"Nah, there was a betting pool going."

"Are you serious?"

"Mmm-hmm. I think Rodney started it."

"I might have to have a word with him…"

John laughed. "Don't bother. Turns out he was right in the end."

"Yes, but he doesn't know that."

He shrugged. "Doesn't matter. Besides, I happen to like the curveballs in life."

"Don't start," Elizabeth warned him. "I've just barely gotten the rules of football down. We're not switching sports already."

John laughed. "Yes, ma'am."

"Ever wonder what else will have changed by the time that we're doing this five years from now?" Elizabeth asked.

"Yeah, sometimes…I know I'm looking forward to it." She nodded, and they both turned back to watch the finale of the fireworks show. They'd been through a lot, and still had quite a few adventures to come.

* * *

FIN. 

Thanks to everyone who came along for the ride with this one. I've appreciated all the feedback I've gotten. And if you haven't left any...that's what the purple button is for 8-)


End file.
